From dded599740ccbb06ad9a26b62d7727ca0d30a172 Mon Sep 17 00:00:00 2001
From: westcott <westcott>
Date: Tue, 8 Feb 2011 16:07:55 +0000
Subject: [PATCH] added homova command

---
 qualityscores.cpp   | 6 ++----
 trimseqscommand.cpp | 6 +++---
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/qualityscores.cpp b/qualityscores.cpp
index 4dd5b38..90412c6 100644
--- a/qualityscores.cpp
+++ b/qualityscores.cpp
@@ -271,12 +271,12 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 		int start = 0;
 		
 		if(seqLength < windowSize) {	return 0;	}
-		
+			
 		while(start < seqLength){
 			double windowSum = 0.0000;
 
 			for(int i=start;i<end;i++){
-				windowSum += qScores[i];				
+				windowSum += qScores[i];
 			}
 			double windowAverage = windowSum / (double)(end-start);
 			
@@ -289,10 +289,8 @@ bool QualityScores::stripQualWindowAverage(Sequence& sequence, int stepSize, int
 			if(end >= seqLength){	end = seqLength - 1;	}
 		}
 		
-		
 		if(end == -1){	end = seqLength;	}
 		
-		
 		sequence.setUnaligned(rawSequence.substr(0,end));
 		trimQScores(-1, end);
 		
diff --git a/trimseqscommand.cpp b/trimseqscommand.cpp
index 2a43e35..7267b91 100644
--- a/trimseqscommand.cpp
+++ b/trimseqscommand.cpp
@@ -207,7 +207,7 @@ TrimSeqsCommand::TrimSeqsCommand(string option)  {
 			temp = validParameter.validFile(parameters, "qthreshold", false);	if (temp == "not found") { temp = "0"; }
 			convert(temp, qThreshold);
 			
-			temp = validParameter.validFile(parameters, "qtrim", false);		if (temp == "not found") { temp = "F"; }
+			temp = validParameter.validFile(parameters, "qtrim", false);		if (temp == "not found") { temp = "t"; }
 			qtrim = m->isTrue(temp);
 
 			temp = validParameter.validFile(parameters, "rollaverage", false);	if (temp == "not found") { temp = "0"; }
@@ -289,7 +289,7 @@ void TrimSeqsCommand::help(){
 		m->mothurOut("The rollaverage parameter allows you to set a minimum rolling average quality score allowed over a window. \n");
 		m->mothurOut("The qstepsize parameter allows you to set a number of bases to move the window over. Default=1.\n");
 		m->mothurOut("The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n");
-		m->mothurOut("The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is F.\n");
+		m->mothurOut("The qtrim parameter will trim sequence from the point that they fall below the qthreshold and put it in the .trim file if set to true. The default is T.\n");
 		m->mothurOut("The keepfirst parameter trims the sequence to the first keepfirst number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements. \n");
 		m->mothurOut("The removelast removes the last removelast number of bases after the barcode or primers are removed, before the sequence is checked to see if it meets the other requirements.\n");
 		m->mothurOut("The trim.seqs command should be in the following format: \n");
@@ -572,7 +572,7 @@ int TrimSeqsCommand::driverCreateTrim(string filename, string qFileName, string
 					else						{	success = 1;				}
 					
 					//you don't want to trim, if it fails above then scrap it
-					if ((!qtrim) && (origLength != currSeq.getNumBases())) { success = 0; }
+					if ((!qtrim) && (origLength != currSeq.getNumBases())) {  success = 0; }
 					
 					if(!success)				{	trashCode += 'q';	}
 				}				
-- 
2.39.2